Difference Between Agarose and Polyacrylamide

Agarose vs Polyacrylamide
 

Agarose and Polyacrylamide are both water-soluble polymers but, between them, many differences can be seen, starting from their origin. Both Agarose and Polyacrylamide have something common in their ability to form porous gel matrices. Despite this, there exist a number of distinct differences between the two. The major differences between both of these polymers lie in their nature of origin, chemical structure, their different uses, and their performance in terms of gel electrophoresis.

What is Agarose?

Agarose is a naturally occurring linear polymer that is in turn derived from a complex polymer called agar found in seaweed. Agarose is extracted from agar by the removal of its protein component called agaropectin. Agarose is what gives agar its ability to form gels.

The major use of agarose is in microbiological and molecular biological studies. In microbiological studies, agarose, when supplemented with suitable nutrients, provides a solid base for cultivating microorganisms such as bacteria and fungi. When used at semi-solid concentrations, it can be useful in assessing the motility of these microorganisms. In molecular biology, it serves as an important tool for one of the most fundamental resolution processes called ‘gel electrophoresis‘ or ‘agarose gel electrophoresis’ (AGE). Gel electrophoresis is a process that allows for resolution or separation of nucleic acids or protein based on their size and charge. Here, agarose serves as a porous sieve-like gel through which separation happens.

Difference Between Agarose and Polyacrylamide

Agarose Structure

What is Polyacrylamide?

Polyacrylamide is a synthetic polymer and is used in a wide variety of industries. As previously mentioned, its use relies on its ability to form gels. However, in addition to this, its ability to retain and drain water at different concentrations is also exploited in various industries.

The most widespread and common use of polyacrylamide is in waste water treatment. Here, it is used as a flocculating agent to remove any suspended organic material; hence, improving turbidity and clarifying the water. Another use of polyacrylamide is in the paper industry. Here, it is used to either retain or drain water from the paper pulp as required. Similarly, in the agricultural and construction industries, it is used as a soil conditioner to prevent soil erosion and improve its quality.

Like agarose, polyacrylamide too is used in molecular biology as an important resolution tool in a similar process called ‘Polyacrylamide gel electrophoresis’ (PAGE). In addition to all of this, Polyacrylamide is also used in ore processing and manufacturing of flocculating agent to remove any suspended organic material; hence, improving turbidity and clarifying the water. Another use of polyacrylamide is in the paper industry. Here, it is used to either retain or drain water from the paper pulp as required. Similarly, in the agricultural and construction industries, it is used as a soil conditioner to prevent soil erosion and improve its quality. In addition to all of this, Polyacrylamide is also used in the manufacturing of food additives, soft contact lenses, and textiles.

 Agarose vs Polyacrylamide

Polyacrylamide Structure

What is the difference between Agarose and Polyacrylamide?

Origin of Agarose and Polyacrylamide:

Agarose: Agarose is a polymer of natural origin. It is derived from seaweed.

Polyacrylamide: Polyacrylamide is of synthetic origin and is not found under any natural circumstance.

Molecular Formula of Agarose and Polyacrylamide:

Agarose: The molecular formula of agarose is  C24H38O19.

Polyacrylamide: The molecular formula of polyacrylamide is (C 3H5NO)n.

Chemical Structure of Agarose and Polyacrylamide:

Agarose: Agarose is a linear polysaccharide. It is made up of repeating disaccharide units called agrobiose held together by hydrogen bonds.

Polyacrylamide: Polyacrylamide is a chemically cross-linked polymer. It is made up of acrylamide monomers and a crosslinking agent N,N’-methylenebisacrylamide.

Toxicity of Agarose and Polyacrylamide:

Agarose: Both agarose and its monomer unit agrobiose are non-toxic in nature.

Polyacrylamide: The monomer unit of polyacrylamide, the acrylamide, is a presumed carcinogen and known neurotoxin while it’s polymerised form is non-toxic in nature.

Characteristics of Agarose and Polyacrylamide Gels:

AGE and PAGE:

Agarose: Agarose gel preparation for AGE is less time consuming, easy and simple, and does not require an initiator or polymerising catalyst.

Polyacrylamide: Polyacrylamide gel preparation for PAGE is time-consuming and tedious and also requires an initiator (ammonium persulphate) and polymerising catalyst (N,N,N’,N’-tetramethylethylendiamine – TEMED).

Nature:

Polyacrylamide gels are chemically more stable than agarose gels.

Pore Size:

Given the same concentration, polyacrylamide gel matrices tend to have smaller pore sizes compared to that of an agarose gel matrix.

Altering Pore Size:

The pore size of polyacrylamide gels can be altered in a more controlled manner than that of agarose gels.

Resolving Power:

Polyacrylamide gels have high resolving power while agarose gels have low resolving power.

Accommodating Nucleic Acid:

Polyacrylamide gels can accommodate larger quantities of nucleic acid than agarose gels for means of resolution.

 

Images Courtesy: Agarose and Structure of polyacrylamide via Wikicommons (Public Domain)